Casualties of War
by xXdreameaterXx
Summary: Post Time War Gallifrey. The Doctor follows a distress signal to the Gallifreyan prison where he finds a newly regenerated Missy who knows him but otherwise suffers from amnesia after being tortured. Who is she and who sent the signal that led him to her? The Doctor might realise too late that there is more than just one enemy after his life. Twelve/Missy AU.
1. Chapter 1

**Summary:** Post Time War Gallifrey. The Doctor follows a distress signal to the dungeons where he finds a newly regenerated Missy, who knows him but otherwise suffers from amnesia after being tortured. Who is she and what was the reason for the signal? The Doctor soon realises there may be more than just one enemy after his life. Twelve/Missy. AU.

_Please note that this is an AU story. The Doctor saved Gallifrey but it's still in the same universe. _

**Casualties of War**

**Chapter 1**

The Doctor was staring at the monitor on his TARDIS console, at the two words flashing in front of his eyes: _help me_. He had checked and double-checked and there could be no doubt. The distress call was coming from Gallifrey.

The Doctor had dreaded going back there after the Time War was over, after he had saved his home planet, afraid they would proclaim him a hero of some sort. From renegade to war hero, an impossible career.

Yet someone on Gallifrey was in need of his help and the Doctor was curious. It wasn't that he had never turned down someone who had asked for his help, but something seemed to be going on on Gallifrey and he needed to know what it was. Several Time Lords, members of the High Council among them, had tried to contact him after the war. He had never replied or accepted their invitation. But this was something else. The message wasn't signed, it wasn't send from the High Council but as he had found out, from the deepest dungeons of the Gallifreyan prison. It had been sending for days and it only ever showed two words: _help me_.

The Doctor let out a grunt as he entered the coordinates into his TARDIS and worked the switches. He would probably regret going back. No good would come of this, he was sure of that. But curiosity always gotten the better of him. The Doctor would have asked Clara for advice, maybe even asked her to come along, but she had been busy with her new love lately and he rarely saw her. And if he did see her, they always seemed to disagree, so he decided it was better to not ask her in the first place.

The Doctor landed in the exact spot from where the distress call was being sent and immediately found the transmitting device strapped to the door of one of the cells. Looking around he realized that he was standing in the wing designed for political prisoners of Gallifrey and as far as he could see only one of the cells was being used. He looked around carefully but couldn't spot a guard anywhere. Later, when he thought about that moment, the Doctor realised that he should have become suspicious right there, head back to the TARDIS and never return to Gallifrey ever again. But as usual he was missing the obvious. The Doctor instead approached the cell door and attempted to look through the small window when he was suddenly blinded by the flash of light caused by regeneration. Whoever was inside that cell was a Time Lord and had just been reborn.

When the light had faded away the Doctor stepped closer again and this time spotted the prisoner. He hadn't exactly thought about what he was going to find following the call for help, but it certainly hadn't been this:

The cell was stark and white. There was no furniture. The only thing inside these walls was a woman, barely dressed in the rags of a former jumpsuit that prisoners on Gallifrey usually wore and she was chained to the wall. The Doctor couldn't take his eyes off her lean body that sat in one of the corners, her back pressed against the wall, her long, dark hair covering most of her face as she stared down to the ground. He felt like he somehow knew her, and then didn't. But she had just regenerated – she could be any Time Lady. He couldn't even tell whether she was still alive. Sure, there had been a regeneration, but there was no movement and then finally the woman lifted her head and stared directly into his eyes.

She tilted her head slightly, as if trying to remember something and after a long while he could see her lips moving, forming the one word that was needed: _Doctor_?

The Doctor pulled out his sonic screwdriver and opened the lock of her cell. To his own surprise there were no alarms, no approaching guards. Nothing happened except the lock opening and the Doctor carefully stepped inside the prison cell.

"Doctor?" the woman asked. Her voice was weak, which wasn't unusual for someone who had just woken up in a whole new body. She stared at him in disbelief.

"Yes?" he asked back, not willing to get any closer. She could be anyone, and if she was down here, there was probably a good reason for it.

"I was hoping you'd come for me," she whispered. Her eyes were unfocused now and the Doctor could tell she was about to slip into unconsciousness.

He knelt down next to her and took her head into his hands, forcing her to look at him further.

"Who are you?" he demanded to know. Her head slipped from his grip, but he held it back up. Only now he noticed the holes that covered her jumpsuit. Burn holes. She had been tortured.

"Please, take me with you," she begged, "Please, Doctor."

The Doctor slapped her cheek gently to keep her awake, but it was too late. The woman was unconscious already. The guards could appear any moment now and the Doctor had a decision to make. Someone on Gallifrey obviously had pity on this woman and wanted the Doctor to save her, and whoever she was, she knew him somehow and had begged him to help her. But it all seemed too easy. The signal had lead him straight to her cell, there were no guards, no alarms, only one prisoner was kept inside these walls. Could it be one of the guards who wanted her rescued? It would make sense. A guard would definitely be able to plant a transmitter and keep the area unoccupied for a while. Yet there still remained the question of her identity. If he was unlucky, he could be bringing the Rani on board of his TARDIS and how would that end?

The Doctor looked back at the woman, who at the moment seemed innocent enough. She was still weakened from her regeneration, or the torture she had been enduring before that. If it was indeed the Rani, it would be easier to throw her out of the TARDIS than carrying her inside.

He activated his sonic again to open the restraints on her wrists and lifted her up, carrying her out of the cell and into his TARDIS. As the door closed behind him, the Doctor could hear the alarm finally going off. Too late, he was already as good as gone.

**OOO**

The man hurried into the chambers of the Lord President in the middle of the night.

"Lord President Rassilon," the man was out of breath from running all the way down to the President's private quarters, "There has been a break-in. It's the Doctor."

Rassilon looked up from his papers. "Did it work? Has he taken the Master?"

"Yes, it appears to have worked. The Master is gone from his cell."

Rassilon smiled, apparently very pleased. "Good. Very good."


	2. Chapter 2

_Reviews already? Thank you guys! I'm glad you like the idea of my FanFic (I like it, too :D )_

**Chapter 2**

The TARDIS was peacefully hovering in the vortex when the woman finally woke up. He had laid her down in his own bed because the TARDIS currently had no other bedroom ready and available. Should she turn out to be a nice Time Lady, he would have to create one for her. As for now, the Doctor was still cautious.

"Good morning," he greeted her when she had finally opened her eyes. The Doctor noticed that they were ice blue and tried to find something familiar in them, but couldn't.

The woman jumped up immediately and started looking around the unfamiliar room.

"Where am I?" she demanded to know.

"Calm down. You're safe. You're in my TARDIS. Nothing will happen to you here," the Doctor said in a low voice, hoping to calm her. He knew that regeneration was never easy and she would be confused no matter what, but this Time Lady had also been imprisoned and tortured for God knows how long. She was bound to be disoriented, "Please, sit back down."

"You came for me," she now stared at him, "I was hoping you'd come. I waited a very long time for you."

"Who are you?"

The woman was stunned into silence by his question. The staring continued, but her gaze seemed empty, as if she was trying very hard to remember. Then suddenly she turned away from him, looking around until she found a mirror. The Doctor watched her as she beheld her own reflection for the first time. She inspected her nose, her cheekbones, her hair. A little embarrassed he averted his eyes when the woman was done admiring her face and went on to feel her own breasts. He cleared his throat.

"Missy," she finally said.

"Missy?" the Doctor asked, "Who's Missy?"

The woman turned around to face him again and shrugged. "I don't know. Me, I guess, whoever that is. You know what it's like, regenerating."

The Doctor was baffled for a moment and shook his head. "What do you mean you don't know? Surely you know who you are. I've never heard of a Time Lady called Missy, so you must be someone else."

Missy let herself fall down unto the bed again and sighed. "Hasn't it ever happened to you, Doctor? You regenerated and for a while forgot who you are?"

He thought about it for a moment. "Yes, you're right. But seriously, is there anything you _do_ know? You seem to know _me_ for a start."

"I'm hungry," was all she replied as she stared at the ceiling of his bedroom. "I want chips. And pancakes."

The Doctor sighed with resignation. He wouldn't get a word out of her before she had eaten. _Women!_

"Okay, here's a suggestion. I'll make you pancakes and as long as I'm in the kitchen, you will take a hot bath and put on some clothes. Deal?"

"Deal," Missy agreed.

"Bathroom and wardrobe are next door. And don't wander off. And don't touch any buttons," he warned her. As long as he wasn't completely sure he could trust her, it was better she didn't fiddle with his TARDIS.

**OOO**

The Doctor had just finished the last pancake when Missy entered the TARDIS kitchen, dressed in one of his best shirts. Other than that, she wore only knickers and socks. His socks.

"Missy," the Doctor stared at her disapprovingly, "That's my shirt."

"Oh," she looked down at herself, "I like it. Can I keep it?"

"For now," he said grumpily and walked over to the cupboard to fetch two plates.

"Where are the chips?" she suddenly seemed disgruntled, "I said I wanted chips."

"And I said I never wanted to go back to Gallifrey because I knew that no good would come of it and here I am - with you on my hands," he pointed at her, "Now eat the pancakes before they get cold."

"And after that we'll have chips?" she asked, sounding hopeful.

"No, after that you tell me everything you know. Then we'll have chips. Maybe."

_Tap. Tap. Tap. Tap. _There was a sudden knock on the door of the TARDIS that caused Missy to drop her fork. Her eyes widened in shock.

"Did you hear that?" she asked the Doctor and it sounded almost as if she expected him to say no.

"Yes, I guess there's someone knocking on the door. Weird, I must have landed accidentally," he explained, "Eat your food. I'll have a look."

When the Doctor opened the door, he found himself in Clara's living room – and an angry Clara standing in front of the TARDIS.

"You're blocking the door," she sounded cross. Why did she always sound cross?

"I, uhm, I landed accidentally. Didn't mean to land in your apartment. I'll be gone in a second," he said quickly and was about to close the door when Clara pushed it back open again.

"It's alright. Park here for as long as you like. I'll be at Danny's place for the whole weekend, I just need to water my plants first," Clara held up a watering can, "I'll just get water from your kitchen."

"No, that's not a good idea," the Doctor blocked the door with his arm. He wasn't exactly sure how Clara would react to an unknown Time Lady in his TARDIS, given the circumstances under which she had come to be there at all. He wasn't keen on a lecture right now.

"Why?" Clara raised an eyebrow.

"You know the, uhm. . . Ood. . . I thought I'd gotten rid of?" he stammered, "Turns out he's still in there and has, uhm, taken the kitchen apart . . . to clean it. No water right now. Sorry. I'll just. . ."

Clara pushed him out of the way before he could stop her. She was too clever to fall for a lie like that. Once she was inside his TARDIS Clara put her arms akimbo.

"What's going on?" she demanded to know.

"I will explain everything to you. Later. I promise. But for now you should probably leave," the Doctor said and looked over Clara's shoulder only to find Missy standing at the other end of the console room.

Clara followed the Doctor's gaze and turned around.

"Mh, that is not how I imagined an Ood to look like," Clara remarked, a smug grin on her face, "And it appears to be wearing your shirt."


	3. Chapter 3

_Thank you guys so much for the reviews! I'm really glad you're enjoying my story :)  
>As for the original Ood incident: There is this minisode called "Pond Life" on YT in which the Doctor has a stray Ood in his TARDIS that keeps wandering off and it stayed with the Ponds for a while until the Doctor picked it up and dropped it off on its home planet. I have this headcanon that the Ood is still somewhere in the TARDIS and just pops up occasionally to wreck havoc with good intentions. I used it in other FanFics already :D<em>

**Chapter 3**

The Doctor grabbed Clara's arm and turned her away from the sight of Missy.

"I can explain everything, but it's a rather long story," the Doctor whispered.

"I bet it is."

"No, you don't understand. I went to Gallifrey last night," the Doctor went on to explain but Clara interrupted him.

"Where else would a Time Lord pick up chicks?"

He groaned. "I found her in prison. She had just regenerated and doesn't remember a thing. I took her with me cause she begged me to."

Clara's eye widened. "Hang on. You brought a prisoner on board of the TARDIS and you have no idea who she is? Doctor, she could be a lunatic."

Missy cleared her throat on the other side of the room. "Do you want me to leave so you can discuss my mental condition in private?"

"Yes, actually, that is a great. . ."

"Shut up, Clara. I have a better idea," the Doctor said and turned to his companion, "Why don't you take Missy to the wardrobe and see if you can find something other for her to wear other than my best shirt?"

"What? Me?" Clara asked in surprise.

"Yes, I think that would be very good. You can dress yourself, can't you? Dressing Missy shouldn't be a problem." his voice suddenly turned into a whisper too low for Missy to hear, "And maybe find out a thing or two about her."

"Alright," Clara replied moodily, "You owe me for this."

Clara headed for the direction of the TARDIS wardrobe, gesturing for Missy to follow her. They walked along the corridors to the room Missy had already seen and she was overwhelmed by the amount of clothing she would have to choose from again. She didn't even know who she was, and not only because of her latest regeneration, so how should she know which outfit was right for her?

"Alright," Clara finally said, searching through the clothes, "Which size are you?"

"No idea," Missy exhaled sharply. All of these clothes looked wrong to her.

"Oh, right. Regeneration. Well, you can hardly walk around in the Doctor's shirt."

"Why not? I like it."

"Because it's his favourite and he told me to dress you up. So, come on."

Missy sighed and approached the clothes rails, flipping through them rather quickly without even really looking.

"I don't like any of them. They're so. . . _girly_," she said, holding up a pink polka dot dress and staring at it in disgust.

"Okay, that one's too girl even for me," Clara replied and put the polka dot dress back it its place, "What do you like then?"

Missy looked around for a while, inspecting her choices closely and walked over to where the Doctor kept his own clothes. She produced a pair of black trousers and another white shirt from the rail.

"These. They'd look nice with a plain jacket," she finally said.

Clara sighed. "These are the Doctor's clothes. Again. And I'm pretty sure that's not what he wants you to wear."

"Well, maybe this regeneration is a cross-dresser."

"I have a proposition for you, Missy. It was Missy, right?"

She nodded in reply and reluctantly hung the clothes back in their place.

"So you remember your name, but nothing else?" Missy noted that Clara's voice had suddenly gone up a pitch. The Doctor had obviously asked Clara to find out more about her.

"No, Missy was just the first thing that came to my mind," she explained. What else could she have told her?

"So you know nothing?" Clara asked, still looking around for a good outfit to put on Missy.

"Not nothing. I know the Doctor. In fact, I know everything about him – and you, Clara Oswald."

Clara turned around, staring at Missy in confusion.

"Me?"

"Clara Oswald, the Doctor's companion," Missy said almost automatically as if the information had been imprinted on her mind.

Clara approached her carefully. "How come you know everything about the Doctor and not yourself?"

"It was the information that was important to them. They wanted to know everything about the Doctor."

"Why?"

"So they could use it to destroy him," Missy wasn't sure how she knew this but she was certain that it was the truth, "They tortured me, hoping I'd give up everything I know."

"And did you?"

"I don't remember," she said and fell silent.

Obviously Clara had realized that she would get no more out of her so she proceeded to look for decent clothes. A few moments later Clara presented her with a pair of black, high waist slacks and a white blouse.

"Here, try these," Clara suggested, "Looks like the female version of the Doctor's outfit. I'm sure you'll look great in it."

"That could work," Missy agreed.

"Now all you need is some eyeliner and lipstick and you'll look like you jumped out of a 50s movie."

**OOO**

"I don't like it," Clara said to the Doctor after she was finished telling the him everything she had learned about Missy.

The Doctor's face had turned into a frown. He was trying to put the pieces of the puzzle together, but it made no sense.

"Okay, we have a Time Lady who knows me very well. For some reason the Time Lords are looking to destroy me, so they capture her and torture her for information, which she might or might not have given up. She can't tell us because she doesn't remember. Then someone plants a distress call that leads me straight to her, making it very easy for me to break her out of prison."

"That sounds like a trap to me," Clara concluded, "You should get rid of her. She regenerated. She could be anyone."

"Yes, she could be, but she is a Time Lady who knows me. And there's only a handful of people that it could be. I don't think one of them would betray me."

"Why would they want to harm you anyway? You _saved_ Gallifrey. They should be grateful," she argued.

"I haven't the foggiest. That is why I want to keep her around. Figure out who she is, maybe when she regains her memory she can tell me what's really going on on Gallifrey," the Doctor said, "I have to know."

"I still don't like it, Doctor. It sounds like you're putting yourself in danger. And me as well. She knows about me. How can she know about me?"

"I don't know, Clara. But I think it would be safer if you stayed home for a while. At least until we have figured out who Missy is."


End file.
